3D0R

Crystal structure of calG3 from Micromonospora echinospora determined in space group P2(1)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	Protein solution (10 mg/mL protein, 0.050 M Sodium chloride, 0.010 M Tris-HCl pH 7.5) mixed in a 1:1 ratio with the Well solution (25% PEG 1500). Cryoprotected in FOMBLIN MW2500, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.44	α = 90
b = 97.677	β = 90.62
c = 63.046	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97918	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.68	50	86.3	0.051	25.11	7		68513

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.68	1.74	43.6		0.496	2.426	3.9	3443

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3D0Q	1.9	38.75	53699	2745	98.032	0.162	0.16	0.212	RANDOM	15.847

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.171		-1.934	-1.774		0.561

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.32
r_dihedral_angle_4_deg	16.414
r_dihedral_angle_3_deg	13.578
r_scangle_it	7.825
r_dihedral_angle_1_deg	7.61
r_scbond_it	5.629
r_mcangle_it	3.006
r_mcbond_it	1.988
r_angle_refined_deg	1.416
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.32
r_dihedral_angle_4_deg	16.414
r_dihedral_angle_3_deg	13.578
r_scangle_it	7.825
r_dihedral_angle_1_deg	7.61
r_scbond_it	5.629
r_mcangle_it	3.006
r_mcbond_it	1.988
r_angle_refined_deg	1.416
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.241
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5754
Nucleic Acid Atoms
Solvent Atoms	579
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.